With Mystery Inc. broken up, the gang decides to check out life after high school and spend a weekend at DARROW COLLEGE. But things don't go as planned when a creature called CHAR GAR GOTHAKON begins terrorizing the campus. Turns out this beast is a fictional character come to life. A creation of the author H.P. HATECRAFT who is a professor at the school.

The gang and original Mystery Incorporated stand before the Evil Entity. The Entity grabs Scooby-Doo, and mentions that he must die and be reborn as a vessel to its darkness. Scooby breaks free, but Pericles volunteers to be possessed by the being, to which the Entity agrees. Professor Pericles believes he has gained ultimate power (due to his growth in size and appearance), but the Evil Entity kills Pericles and mutates his body into a squid-like monster. The Entity then assumes control of the Kriegstaffelbots and summons other evil Anunnaki, who proceed to offer the townspeople for the Entity to consume. When Scooby destroys the sarcophagus, the Entity is killed and a vortex sucks everything in, except for the gang, then explodes. The gang find themselves in a new version of Crystal Cove and Earth itself. After some strange encounters, Mystery Incorporated realizes that all the evil ever caused by the Entity has come undone, thereby changing history.